I have had to do this sort of thing hundreds of times.  Doing it "by hand" eg in Illustrator is an option, but it is error-prone and time-consuming for big trees.  And then, next week when you add another taxon you will need to do it all again!  Some time ago I put together a little tutorial and worked example for doing it programmatically, using p4.

http://p4.nhm.ac.uk/tutorial/combine_supports.html

Bootstrap values of totally different approaches in one phylogeny? I don't know any programme which can combine trees of different approaches and plot the according supportvalues on the branches for each analysis.

Just do it manually, it is very fast and easy. Perform all the analyses, choose one tree and open it e.g. with TreeGraph 2 and work with the tree. With TreeGraph 2 you can easy work with the tree (insert all supportvalues, indicate clades etc. with brackets, a lot of different stuff you can do). It is not a lot work more as you need to refurbish your tree anyway for a publication

Thank you so much Sebastian. I found this is very useful.

Exactly as Sebastian says. Another option for tree manipulation program is FigTree (http://tree.bio.ed.ac.uk/software/figtree/) although I'm not sure you can manually edit the node support values....

Thank Daniel John Jackson. I'll try it out! I have this program ready on my computer but never even know how to use.

 I agree with Daniel, Fig tree is a very useful program for edition of trees, however it only allow to add one kind of support value in you trees each time, in one of my papers that is in press I used Bayesian and Parsimony with jackniffe values and Bremer values, even with implied weighting and at the end I had to editing manually these different  support values on my final tree, is is a little tricky but you canb use a lot of softwares like Photoshop, Illustrator or Corel.

I use FigTree to display the set of support values that corresponds with the tree I am presenting, then save the tree as a PDF--that makes it much easier to edit the tree in Adobe Illustrator/Photoshop/Acrobat when adding support values from other analyses. 

I like Illustrator best for editing trees because it is easy to scale the tree and change line weights, but it is expensive. Haven't used Inkspace yet, but I hear its powerful and a much cheaper alternative to Illustrator for vector graphics. Alternatively, you can add the support values in R if you have some programming experience with R--there are lots of tutorials available.

New update, I've also become a big fan of The Interactive Tree of Life https://itol.embl.de/ -- free, online tree-editing tool. Its pretty powerful and works particularly well for very large trees that aren't practical to work with in FigTree. Very user friendly too.

You can use open source alternatives of Illustrator etc. Inkscape is relatively intuitive and works great for editing trees. Just export your tree from Figtree or any other tree visualiser in a vector graphic format (ps, svg, pdf) and import to Inkscape. Then you can add any information you like.

For all of you using FigTree:

I also use FigTree for fast and easy display of trees. However, if you really want to work with the tree FigTree is very limited, try TreeGraph2. You need a little bit effort to get into TreeGraph2, but it is worth it. It is like Paint (FigTree) vs. Photoshop (TreeGraph2)

I have had to do this sort of thing hundreds of times.  Doing it "by hand" eg in Illustrator is an option, but it is error-prone and time-consuming for big trees.  And then, next week when you add another taxon you will need to do it all again!  Some time ago I put together a little tutorial and worked example for doing it programmatically, using p4.

http://p4.nhm.ac.uk/tutorial/combine_supports.html

You can add your values in FigTree by setting Selection Mode to Node. Then you select each node individually and use Annotate to add your information to the selected node. This will only work for a tree with a small number of branches. It will be very time consuming for large trees.

I use Adobe Illustrator!

As the others say, for relatively small trees the best you can do is export from FigTree your consensus tree in PDF format and then add the multiple support values on each branch with graphical software, but for big trees this is a very time consuming task. As far as I know TreeGraph2 is the only program that allows multiple values on branches and creates a consensus tree from different tree files.

Hi,

If you don't want to use other software you can do by hand. From my experience, I copied the tree structure from MEGA5 (no legend, no bootstrap values, which is possible in options) into power point, then add all legends, strains name, and bootstrap value by hand. It is very time consuming but it as the advantage to be editable and adjusted for publication if required. Once the tree complete you export as pdf, open it in photoshop then save as jpeg of other file type.

Check the tree in this paper, look nice isn't it? :)

Best regards,

Article The phylogenetic position and phenotypic changes of a Chlore...

If you know somebody that uses R, ask him nicely. The package ggtree can annotate everything to a tree, even piecharts.

If you have tree files containing support values generated with multiple methods, you can use my software TreeGraph 2 to combine all these into one tree file. Depending on possible differences between the tree topologies, support values will be displayed as supporting or conflicting as described here: http://treegraph.bioinfweb.info/Help/wiki/Adding_support_values#How_are_support_values_merged.3F

You can also interactively compare trees, before merging them as explained here: http://treegraph.bioinfweb.info/Help/wiki/Synchronizing_tree_selections

After the trees are merged, the different support values can be positioned in different ways on the branches. There is also a video tutorial on that available. http://treegraph.bioinfweb.info/Help/wiki/Tutorial:Adding_support_values

Best, Ben

http://treegraph.bioinfweb.info/Help/wiki/Adding_support_values#How_are_support_values_merged.3F

http://treegraph.bioinfweb.info/Help/wiki/Synchronizing_tree_selections

http://treegraph.bioinfweb.info/Help/wiki/Tutorial:Adding_support_values

Article TreeGraph 2: combining and visualizing evidence from differe...

Poster New comparison and annotation methods of the phylogenetic tr...

One can consider using the server as follows.

http://www.thines-lab.senckenberg.de/trease/

That is a server for building phylogenetic trees from the scratch, and when more than one method for phylogenetic tree construction is opted, it gives an option to merge and reflect the confidence values in one primary tree.

@ Bagdevi Mishra

That sounds very interesting. Is there a description of the algorithm how support values are merged? Do you know in which format the merged output is provided? As a graphic or using a metadata-rich format?